[English] 日本語
Yorodumi
- PDB-6ea4: ERAP2 bound to Aryl Sulfonamide Uncompetitive Inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ea4
TitleERAP2 bound to Aryl Sulfonamide Uncompetitive Inhibitor
ComponentsEndoplasmic reticulum aminopeptidase 2
KeywordsHYDROLASE/INHIBITOR / Inhibitor / Immunity / Aminopeptidase / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / antigen processing and presentation of peptide antigen via MHC class I / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / metallopeptidase activity ...Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / antigen processing and presentation of peptide antigen via MHC class I / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / metallopeptidase activity / endopeptidase activity / adaptive immune response / endoplasmic reticulum lumen / endoplasmic reticulum membrane / proteolysis / extracellular space / zinc ion binding / membrane / cytoplasm
Similarity search - Function
Zincin-like fold - #20 / Immunoglobulin-like - #1910 / Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Zincin-like fold / tricorn interacting facor f3 domain / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase ...Zincin-like fold - #20 / Immunoglobulin-like - #1910 / Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Zincin-like fold / tricorn interacting facor f3 domain / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
IMIDAZOLE / Chem-J2G / LYSINE / TRIETHYLENE GLYCOL / Endoplasmic reticulum aminopeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMaben, Z. / Stern, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI153828 United States
CitationJournal: To Be Published
Title: Crystal structure of human ER aminopeptidase 1 bound to aryl sulfonamide inhibitor.
Authors: Maben, Z. / Stern, L.J.
History
DepositionAug 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity_name_com.entity_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Jun 15, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / cell / chem_comp / database_2 / diffrn / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_branch_scheme / pdbx_contact_author / pdbx_entity_branch_descriptor / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / symmetry
Item: _audit_author.identifier_ORCID / _cell.volume ..._audit_author.identifier_ORCID / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn.pdbx_serial_crystal_experiment / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _pdbx_audit_support.grant_number / _pdbx_branch_scheme.auth_asym_id / _pdbx_branch_scheme.auth_seq_num / _pdbx_contact_author.id / _pdbx_entity_branch_descriptor.descriptor / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.pdbx_CC_half / _reflns.pdbx_CC_star / _reflns.pdbx_Rmerge_I_obs / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id / _symmetry.space_group_name_Hall
Description: Ligand geometry
Details: An alternate conformation for the bound phenylsulfamoyl benzoic acid inhibitor was included at partial occupancy, with piperidine and trifluoromethylphenyl rings flipped.
Provider: author / Type: Coordinate replacement
Revision 3.1Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endoplasmic reticulum aminopeptidase 2
B: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,81231
Polymers210,2322
Non-polymers8,58029
Water3,765209
1
A: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,96617
Polymers105,1161
Non-polymers4,85016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,84614
Polymers105,1161
Non-polymers3,73013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.233, 135.453, 127.283
Angle α, β, γ (deg.)90.000, 90.110, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 54 through 134 or (resid 135...
d_2ens_1(chain "B" and (resid 54 through 135 or (resid 136...
d_1ens_2chain "C"
d_2ens_2chain "D"
d_3ens_2chain "G"
d_1ens_3chain "E"
d_2ens_3chain "F"
d_3ens_3chain "I"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROPHEA2 - 124
d_12ens_1GLYPHEA126 - 361
d_13ens_1ASPILEA363 - 427
d_14ens_1TYRASNA429 - 449
d_15ens_1VALTRPA454 - 497
d_16ens_1ALATHRA499 - 514
d_17ens_1ASNASPA518 - 533
d_18ens_1THRHISA538 - 628
d_19ens_1METALAA630 - 783
d_110ens_1ARGARGA785 - 815
d_111ens_1ILEARGA817 - 881
d_112ens_1ZNZNA
d_113ens_1MESMESA
d_114ens_1LYSLYSA4
d_115ens_1NAGNAGA
d_116ens_1NAGNAGA
d_117ens_1NAGNAGA
d_21ens_1PROPHEB1 - 123
d_22ens_1GLYPHEB125 - 360
d_23ens_1ASPILEB362 - 426
d_24ens_1TYRTRPB428 - 492
d_25ens_1ALAHISB494 - 616
d_26ens_1METALAB618 - 771
d_27ens_1ARGARGB773 - 803
d_28ens_1ILEARGB805 - 869
d_29ens_1ZNZNB
d_210ens_1MESMESB
d_211ens_1LYSLYSB4
d_212ens_1NAGNAGB
d_213ens_1NAGNAGB
d_214ens_1NAGNAGB
d_11ens_2NAGNAGC
d_12ens_2NAGNAGC
d_13ens_2BMABMAC
d_14ens_2MANMANC
d_15ens_2MANMANC
d_21ens_2NAGNAGD
d_22ens_2NAGNAGD
d_23ens_2BMABMAD
d_24ens_2MANMAND
d_25ens_2MANMAND
d_31ens_2NAGNAGE
d_32ens_2NAGNAGE
d_33ens_2BMABMAE
d_34ens_2MANMANE
d_35ens_2MANMANE
d_11ens_3NAGNAGF
d_12ens_3NAGNAGF
d_21ens_3NAGNAGG
d_22ens_3NAGNAGG
d_31ens_3NAGNAGH
d_32ens_3NAGNAGH

NCS ensembles :
ID
ens_1
ens_2
ens_3

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Endoplasmic reticulum aminopeptidase 2 / Leukocyte-derived arginine aminopeptidase / L-RAP


Mass: 105116.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERAP2, LRAP / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q6P179, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

-
Sugars , 4 types, 14 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#9: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 8 types, 224 molecules

#5: Chemical ChemComp-ZN / ZINC ION / Leukocyte-derived arginine aminopeptidase / L-RAP


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-J2G / 4-methoxy-3-{[2-(piperidin-1-yl)-4-(trifluoromethyl)phenyl]sulfamoyl}benzoic acid


Mass: 458.451 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C20H21F3N2O5S / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H5N2
#11: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#12: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.38 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG 8000, 20% ethylene glycol, 61 mM MES, 39 mM imidazole, 20 mM sodium-L-glutamate, 20 mM D-L-alanine, 20 mM glycine, 20 mM D-L-lysine, 20 mM D-L-serine (Morpheus H2)
Temp details: room temperature

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 29, 2016
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.45→29.895 Å / Num. obs: 90906 / % possible obs: 97.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 54.25 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.08731 / Rpim(I) all: 0.05 / Rrim(I) all: 0.097 / Rsym value: 0.071 / Net I/av σ(I): 10 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.451-2.583.81.0440.8135960.6871.3551.04499.7
2.58-2.743.80.6521.2128250.4350.8560.65299.6
2.74-2.933.80.3852120800.2550.5040.38599.9
2.93-3.163.80.2133.7112980.1420.280.213100
3.16-3.473.80.112795960.0760.1490.11292.3
3.47-3.873.80.05713.484760.0390.0770.05790.2
3.87-4.473.80.0381878300.0260.0520.03894.1
4.47-5.483.70.0332070020.0230.0450.03399.7
5.48-7.753.80.02922.454570.0210.0410.02999.8
7.75-29.8953.60.02129.227460.0160.0310.02190.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
XDSMarch 30, 2013data reduction
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SE6

3se6


Resolution: 2.45→29.29 Å / SU ML: 0.3079 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.8038
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2361 2027 2.23 %
Rwork0.208 88709 -
obs0.2087 90736 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.35 Å2
Refinement stepCycle: LAST / Resolution: 2.45→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14209 0 560 209 14978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001815247
X-RAY DIFFRACTIONf_angle_d0.48720683
X-RAY DIFFRACTIONf_chiral_restr0.03962359
X-RAY DIFFRACTIONf_plane_restr0.00312537
X-RAY DIFFRACTIONf_dihedral_angle_d11.76875691
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS2.65688956433
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS3.12758720518
ens_2d_3CX-RAY DIFFRACTIONTorsion NCS1.00641182782
ens_3d_2DX-RAY DIFFRACTIONTorsion NCS0.705318159502
ens_3d_3EX-RAY DIFFRACTIONTorsion NCS0.476509092896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.510.3591470.32116455X-RAY DIFFRACTION98.68
2.51-2.580.38531460.32716462X-RAY DIFFRACTION99.62
2.58-2.660.33981460.30356481X-RAY DIFFRACTION99.61
2.66-2.740.28921480.28646437X-RAY DIFFRACTION99.28
2.74-2.840.29031520.26796493X-RAY DIFFRACTION99.86
2.84-2.950.28351440.25316515X-RAY DIFFRACTION99.89
2.95-3.090.24141460.246510X-RAY DIFFRACTION99.91
3.09-3.250.26131620.23326487X-RAY DIFFRACTION99.92
3.25-3.450.26661360.23075745X-RAY DIFFRACTION87.97
3.45-3.720.23691340.20975619X-RAY DIFFRACTION86.29
3.72-4.090.20311260.19316052X-RAY DIFFRACTION92.61
4.09-4.680.22431480.16596561X-RAY DIFFRACTION99.84
4.68-5.890.21761480.17356530X-RAY DIFFRACTION99.75
5.89-29.290.17641440.1746362X-RAY DIFFRACTION95.72
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.70928347576-0.565470059817-0.4763393150522.52609391902-0.05212464668391.268760347910.1222067052650.0942668849840.0849739306185-0.0336965230928-0.0817484010948-0.7040872403050.1706609205270.4666471552-0.03666740036120.3098725490120.08843089749750.02995577147790.4386996828710.008608081091520.47892488323936.125-15.366132.748
22.31880556947-1.080463797730.2335850685123.84940956762-0.06514534939893.324422928540.0743704192915-0.058069544336-0.3588015433560.0778946003753-0.1015776002780.6425626784850.262689578649-0.2011204968490.03856493832510.254554871403-0.03210969090870.03842841852180.312134253922-0.008773287296610.4713507628849.4-14.213133.123
31.1061775977-1.570379686130.4831520149655.46854654499-0.3827509838681.944119200860.1622748921260.244885581842-0.0295667066192-0.471313304121-0.1979611976440.1208828047520.05587382109180.03343205939170.02057269539620.2718249730010.0129211385927-0.0259687040040.3764274418680.009669742222540.24558246977311.966-0.332122.155
42.52082252447-1.37280511030.8338014161423.48042359003-0.6151500645731.666691692590.3943246999410.6969786224830.391331414269-1.04189894385-0.484331030137-0.05201555445-0.1628143269560.08500597257720.09241423962270.7343130810390.1716921882360.09133371815570.6728688422870.1115791913320.4042243484314.027.928109.364
52.14034752006-1.13694098422-0.2589281437613.30203517752-0.0959946184143.020167505530.2681496992320.5998742153730.135876200503-0.857231038667-0.3086984818290.674660521982-0.169954669357-0.1833945418780.03911201454330.5059975361980.119979497769-0.173647393310.505785750630.08442771439470.583525498051-3.09118.834115.17
62.656469910460.526393129044-0.5524522689943.50216387248-1.236313771982.57444847194-0.24099585623-0.0685386536754-0.1538627715260.6111804871390.1555610239630.884638238333-0.221423374915-0.3501847805110.04596626868580.4334368082070.08539844861530.2163023461910.4734247074540.05593904170990.781037115638-8.56915.06141.267
73.00941141375-2.012035791911.152009499523.144843057490.02635450077712.33798371808-0.338541036292-0.60873447033-0.2570841742261.205205640060.4374331551680.545812672977-0.15482900927-0.214632697728-0.1112757617740.6009408314530.0333517129770.2625294799820.4901147462240.1098561023370.490871266082.1385.172151.092
84.370040908080.250052890028-2.239488964555.23404316808-2.016724369034.21329954555-0.29797773653-0.3784411752720.456169801320.7247189825830.078743780779-0.171204543335-0.3725746991170.4210674318080.2029449258130.492393326889-0.0232196366555-0.125244913680.430978330981-0.03225078275240.37702079329118.47713.305146.305
93.44198870419-4.241080442490.6351578147255.14950614522-0.6033854023681.987078583530.1139062506340.2066863053180.429370970899-0.00249233919667-0.229399078401-0.567006801602-0.2689250497430.4002311901330.1166229855620.384618898637-0.1184878558880.02185508340980.3750800428040.1068081297560.57314303825615.60524.674131.486
101.84603452735-0.008112650576790.6231994057711.955028945020.7884060480291.99796298971-0.0874791405357-0.3009573754540.4169232425730.0307707709950.1403262862260.356859734411-0.126100083263-0.248609169404-0.06165958149190.786980543875-0.1696223359140.2851068371590.336798398946-0.004111125571230.9532790796669.1853.981130.426
114.193690769511.028096620620.05894200651944.165667141820.549098630772.314214287290.539743527864-0.830641588656-0.4314183618840.936856607085-0.486319239230.8409574530460.522267707958-0.660368308918-0.03435415430020.835846445777-0.2563285848510.04477948295260.6862698511090.07621711791640.5897137924392.123-21.976179.781
123.06920326089-0.04401827456641.359515914492.65046215065-1.115651069544.61607325050.40781493469-0.358831081833-0.8697819201650.771138114452-0.118564188978-1.25456777180.7194645011960.178479128328-0.1540337348860.847291731666-0.0222653069176-0.3654647487880.5163149157940.06033321616340.87689459349628.91-20.842179.489
131.925170258910.5097757660560.6973686482791.067436336680.04273902721861.603639065980.58233308304-1.333454616310.05717719710811.61846082522-0.543985301066-0.478992209970.318649945337-0.316265946184-0.02764104549191.83709811817-0.402456602049-0.3297219019691.335092133310.02411137210590.70805301219625.821-8.185202.813
140.476685393169-0.8116478525830.3424034852981.25025103494-0.6153845837791.56106525250.513101984713-1.242504692380.1074147761191.37225213641-0.583157363347-0.8712146754670.0368584294369-0.2372798133690.06843173103331.85862342964-0.452976966156-0.64636332431.52566129192-0.1733497531021.2252717381442.0756.171207.616
150.853195073998-0.153565635022-0.7668128579684.371099396272.576593443063.538720760590.396028777977-0.3327264718180.305055674590.008004860731170.0190158815743-1.36301925261-0.5666315796010.529766446405-0.3493382587960.935079735014-0.134525251197-0.3283920784440.803229537732-0.2471276629261.2895357795143.66813.262187.341
167.448398697731.386205537442.876040193425.237870440641.600982012814.37414339302-0.2253791926390.581483254387-0.0636897799376-0.3717719073960.65456738763-1.3951101082-0.5756510933650.878874613963-0.4268283943490.616861985145-0.150268182320.08177548621340.659468934009-0.1946201364810.88523386827640.214.443170.9
177.585662211341.48884802428-0.6818958835197.76923466851.761589634125.40188765044-0.529135522451-0.1109172265251.41159410137-0.2610064478760.160276711630.469098825171-0.912919656223-0.080206972260.3556842346550.6978443591550.0411596370625-0.1831809719410.426324063453-0.008933110263190.64540383908619.4179.21174.421
182.793753136772.86874548421.442459050632.861247706181.101434237432.749952909710.216039525862-0.7852347583621.143054963520.704297120689-0.5205297039660.552685783247-0.173728636271-0.4450983258270.3353790907381.003507050580.0316650953769-0.02378564035160.833566166797-0.4592587408931.0699225036121.91116.007191.906
191.84247794365-1.399596400060.2668374344961.14832979662-0.5760227810711.09633080430.162199608131-1.407330115370.5593666793190.2675281205670.060677712472-0.202859359127-0.127110544014-0.0172700827872-0.2503331382861.68209789869-0.148741349568-0.1356900870951.10107399608-0.2862713177930.9593146340822.694-4.385196.008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 53:271 )A53 - 271
2X-RAY DIFFRACTION2( CHAIN A AND RESID 272:357 )A272 - 357
3X-RAY DIFFRACTION3( CHAIN A AND RESID 358:442 )A358 - 442
4X-RAY DIFFRACTION4( CHAIN A AND RESID 443:594 )A443 - 594
5X-RAY DIFFRACTION5( CHAIN A AND RESID 595:713 )A595 - 713
6X-RAY DIFFRACTION6( CHAIN A AND RESID 714:780 )A714 - 780
7X-RAY DIFFRACTION7( CHAIN A AND RESID 781:830 )A781 - 830
8X-RAY DIFFRACTION8( CHAIN A AND RESID 831:891 )A831 - 891
9X-RAY DIFFRACTION9( CHAIN A AND RESID 892:963 )A892 - 963
10X-RAY DIFFRACTION10( CHAIN A AND RESID 1004:1009 )A1004 - 1009
11X-RAY DIFFRACTION11( CHAIN B AND RESID 54:271 )B54 - 271
12X-RAY DIFFRACTION12( CHAIN B AND RESID 272:357 )B272 - 357
13X-RAY DIFFRACTION13( CHAIN B AND RESID 358:605 )B358 - 605
14X-RAY DIFFRACTION14( CHAIN B AND RESID 606:692 )B606 - 692
15X-RAY DIFFRACTION15( CHAIN B AND RESID 693:744 )B693 - 744
16X-RAY DIFFRACTION16( CHAIN B AND RESID 745:830 )B745 - 830
17X-RAY DIFFRACTION17( CHAIN B AND RESID 831:891 )B831 - 891
18X-RAY DIFFRACTION18( CHAIN B AND RESID 892:961 )B892 - 961
19X-RAY DIFFRACTION19( CHAIN B AND RESID 1004:1007 )B1004 - 1007

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more